!14267 add unet++ 310 mindir infer and update unet 310 infer code

From: @lihongkang1
Reviewed-by: @c_34,@wuxuejian
Signed-off-by: @c_34

model_zoo/official/cv/unet/ascend310_infer/src/main.cc

@@ -42,11 +42,17 @@ using mindspore::MSTensor;
 using mindspore::ModelType;
 using mindspore::GraphCell;
 using mindspore::kSuccess;
+using mindspore::dataset::vision::Decode;
+using mindspore::dataset::vision::SwapRedBlue;
+using mindspore::dataset::vision::Normalize;
+using mindspore::dataset::vision::Resize;
+using mindspore::dataset::vision::HWC2CHW;
 
 
 DEFINE_string(mindir_path, "", "mindir path");
 DEFINE_string(dataset_path, ".", "dataset path");
 DEFINE_int32(device_id, 0, "device id");
+DEFINE_string(need_preprocess, "n", "need preprocess or not");
 
 int main(int argc, char **argv) {
   gflags::ParseCommandLineFlags(&argc, &argv, true);
@@ -78,6 +84,14 @@ int main(int argc, char **argv) {
 
   std::map<double, double> costTime_map;
   size_t size = all_files.size();
+
+  auto decode(new Decode());
+  auto swapredblue(new SwapRedBlue());
+  auto resize(new Resize({96, 96}));
+  auto normalize(new Normalize({127.5, 127.5, 127.5}, {127.5, 127.5, 127.5}));
+  auto hwc2chw(new HWC2CHW());
+  Execute preprocess({decode, swapredblue, resize, normalize, hwc2chw});
+
   for (size_t i = 0; i < size; ++i) {
     struct timeval start = {0};
     struct timeval end = {0};
@@ -86,7 +100,17 @@ int main(int argc, char **argv) {
     std::vector<MSTensor> inputs;
     std::vector<MSTensor> outputs;
     std::cout << "Start predict input files:" << all_files[i] << std::endl;
-    auto img = ReadFileToTensor(all_files[i]);
+
+    auto img = MSTensor();
+    if (FLAGS_need_preprocess == "y") {
+      ret = preprocess(ReadFileToTensor(all_files[i]), &img);
+      if (ret != kSuccess) {
+        std::cout << "preprocess " << all_files[i] << " failed." << std::endl;
+        return 1;
+      }
+    } else {
+      img = ReadFileToTensor(all_files[i]);
+    }
 
     inputs.emplace_back(model_inputs[0].Name(), model_inputs[0].DataType(), model_inputs[0].Shape(),
            img.Data().get(), img.DataSize());

model_zoo/official/cv/unet/export.py

@@ -21,6 +21,7 @@ from mindspore import Tensor, export, load_checkpoint, load_param_into_net, cont
 from src.unet_medical.unet_model import UNetMedical
 from src.unet_nested import NestedUNet, UNet
 from src.config import cfg_unet as cfg
+from src.utils import UnetEval
 
 parser = argparse.ArgumentParser(description='unet export')
 parser.add_argument("--device_id", type=int, default=0, help="Device id")
@@ -52,5 +53,6 @@ if __name__ == "__main__":
     param_dict = load_checkpoint(args.ckpt_file)
     # load the parameter into net
     load_param_into_net(net, param_dict)
+    net = UnetEval(net)
     input_data = Tensor(np.ones([args.batch_size, cfg["num_channels"], args.height, args.width]).astype(np.float32))
     export(net, input_data, file_name=args.file_name, file_format=args.file_format)

model_zoo/official/cv/unet/postprocess.py

@@ -15,53 +15,77 @@
 """unet 310 infer."""
 import os
 import argparse
+import cv2
 import numpy as np
 
-from src.data_loader import create_dataset
+from src.data_loader import create_dataset, create_cell_nuclei_dataset
 from src.config import cfg_unet
-from scipy.special import softmax
 
 
 class dice_coeff():
     def __init__(self):
         self.clear()
-
     def clear(self):
         self._dice_coeff_sum = 0
+        self._iou_sum = 0
         self._samples_num = 0
 
     def update(self, *inputs):
         if len(inputs) != 2:
-            raise ValueError('Mean dice coefficient need 2 inputs (y_pred, y), but got {}'.format(len(inputs)))
-
-        y_pred = inputs[0]
+            raise ValueError('Need 2 inputs ((y_softmax, y_argmax), y), but got {}'.format(len(inputs)))
         y = np.array(inputs[1])
-
         self._samples_num += y.shape[0]
-        y_pred = y_pred.transpose(0, 2, 3, 1)
         y = y.transpose(0, 2, 3, 1)
-        y_pred = softmax(y_pred, axis=3)
-
+        b, h, w, c = y.shape
+        if b != 1:
+            raise ValueError('Batch size should be 1 when in evaluation.')
+        y = y.reshape((h, w, c))
+        if cfg_unet["eval_activate"].lower() == "softmax":
+            y_softmax = np.squeeze(inputs[0][0], axis=0)
+            if cfg_unet["eval_resize"]:
+                y_pred = []
+                for m in range(cfg_unet["num_classes"]):
+                    y_pred.append(cv2.resize(np.uint8(y_softmax[:, :, m] * 255), (w, h)) / 255)
+                y_pred = np.stack(y_pred, axis=-1)
+            else:
+                y_pred = y_softmax
+        elif cfg_unet["eval_activate"].lower() == "argmax":
+            y_argmax = np.squeeze(inputs[0][1], axis=0)
+            y_pred = []
+            for n in range(cfg_unet["num_classes"]):
+                if cfg_unet["eval_resize"]:
+                    y_pred.append(cv2.resize(np.uint8(y_argmax == n), (w, h), interpolation=cv2.INTER_NEAREST))
+                else:
+                    y_pred.append(np.float32(y_argmax == n))
+            y_pred = np.stack(y_pred, axis=-1)
+        else:
+            raise ValueError('config eval_activate should be softmax or argmax.')
+        y_pred = y_pred.astype(np.float32)
         inter = np.dot(y_pred.flatten(), y.flatten())
         union = np.dot(y_pred.flatten(), y_pred.flatten()) + np.dot(y.flatten(), y.flatten())
 
         single_dice_coeff = 2*float(inter)/float(union+1e-6)
-        print("single dice coeff is:", single_dice_coeff)
+        single_iou = single_dice_coeff / (2 - single_dice_coeff)
+        print("single dice coeff is: {}, IOU is: {}".format(single_dice_coeff, single_iou))
         self._dice_coeff_sum += single_dice_coeff
+        self._iou_sum += single_iou
 
     def eval(self):
         if self._samples_num == 0:
             raise RuntimeError('Total samples num must not be 0.')
-
-        return self._dice_coeff_sum / float(self._samples_num)
+        return (self._dice_coeff_sum / float(self._samples_num), self._iou_sum / float(self._samples_num))
 
 
 def test_net(data_dir,
              cross_valid_ind=1,
              cfg=None):
 
-    _, valid_dataset = create_dataset(data_dir, 1, 1, False, cross_valid_ind, False, do_crop=cfg['crop'],
-                                      img_size=cfg['img_size'])
+    if 'dataset' in cfg and cfg['dataset'] == "Cell_nuclei":
+        valid_dataset = create_cell_nuclei_dataset(data_dir, cfg['img_size'], 1, 1, is_train=False,
+                                                   eval_resize=cfg["eval_resize"], split=0.8)
+    else:
+        _, valid_dataset = create_dataset(data_dir, 1, 1, False, cross_valid_ind, False, do_crop=cfg['crop'],
+                                          img_size=cfg['img_size'])
     labels_list = []
 
     for data in valid_dataset:
@@ -89,10 +113,25 @@ if __name__ == '__main__':
     rst_path = args.rst_path
     metrics = dice_coeff()
 
-    for j in range(len(os.listdir(rst_path))):
-        file_name = rst_path + "ISBI_test_bs_1_" + str(j) + "_0" + ".bin"
-        output = np.fromfile(file_name, np.float32).reshape(1, 2, 576, 576)
-        label = label_list[j]
-        metrics.update(output, label)
-
-    print("Cross valid dice coeff is: ", metrics.eval())
+    if 'dataset' in cfg_unet and cfg_unet['dataset'] == "Cell_nuclei":
+        for i, bin_name in enumerate(os.listdir('./preprocess_Result/')):
+            bin_name_softmax = bin_name.replace(".png", "") + "_0.bin"
+            bin_name_argmax = bin_name.replace(".png", "") + "_1.bin"
+            file_name_sof = rst_path + bin_name_softmax
+            file_name_arg = rst_path + bin_name_argmax
+            softmax_out = np.fromfile(file_name_sof, np.float32).reshape(1, 96, 96, 2)
+            argmax_out = np.fromfile(file_name_arg, np.float32).reshape(1, 96, 96)
+            label = label_list[i]
+            metrics.update((softmax_out, argmax_out), label)
+    else:
+        for j in range(len(os.listdir('./preprocess_Result/'))):
+            file_name_sof = rst_path + "ISBI_test_bs_1_" + str(j) + "_0" + ".bin"
+            file_name_arg = rst_path + "ISBI_test_bs_1_" + str(j) + "_1" + ".bin"
+            softmax_out = np.fromfile(file_name_sof, np.float32).reshape(1, 576, 576, 2)
+            argmax_out = np.fromfile(file_name_arg, np.float32).reshape(1, 576, 576)
+            label = label_list[j]
+            metrics.update((softmax_out, argmax_out), label)
+
+    eval_score = metrics.eval()
+    print("============== Cross valid dice coeff is:", eval_score[0])
+    print("============== Cross valid IOU is:", eval_score[1])

model_zoo/official/cv/unet/preprocess.py

@@ -14,6 +14,10 @@
 # ============================================================================
 """unet 310 infer preprocess dataset"""
 import argparse
+import os
+import numpy as np
+import cv2
+
 from src.data_loader import create_dataset
 from src.config import cfg_unet
 
@@ -29,6 +33,56 @@ def preprocess_dataset(data_dir, result_path, cross_valid_ind=1, cfg=None):
         data[0].asnumpy().tofile(file_path)
 
 
+class CellNucleiDataset:
+    """
+    Cell nuclei dataset preprocess class.
+    """
+    def __init__(self, data_dir, repeat, result_path, is_train=False, split=0.8):
+        self.data_dir = data_dir
+        self.img_ids = sorted(next(os.walk(self.data_dir))[1])
+        self.train_ids = self.img_ids[:int(len(self.img_ids) * split)] * repeat
+        np.random.shuffle(self.train_ids)
+        self.val_ids = self.img_ids[int(len(self.img_ids) * split):]
+        self.is_train = is_train
+        self.result_path = result_path
+        self._preprocess_dataset()
+
+    def _preprocess_dataset(self):
+        for img_id in self.val_ids:
+            path = os.path.join(self.data_dir, img_id)
+            img = cv2.imread(os.path.join(path, "images", img_id + ".png"))
+            if len(img.shape) == 2:
+                img = np.expand_dims(img, axis=-1)
+                img = np.concatenate([img, img, img], axis=-1)
+            mask = []
+            for mask_file in next(os.walk(os.path.join(path, "masks")))[2]:
+                mask_ = cv2.imread(os.path.join(path, "masks", mask_file), cv2.IMREAD_GRAYSCALE)
+                mask.append(mask_)
+            mask = np.max(mask, axis=0)
+            cv2.imwrite(os.path.join(self.result_path, img_id + ".png"), img)
+
+    def _read_img_mask(self, img_id):
+        path = os.path.join(self.data_dir, img_id)
+        img = cv2.imread(os.path.join(path, "image.png"))
+        mask = cv2.imread(os.path.join(path, "mask.png"), cv2.IMREAD_GRAYSCALE)
+        return img, mask
+
+    def __getitem__(self, index):
+        if self.is_train:
+            return self._read_img_mask(self.train_ids[index])
+        return self._read_img_mask(self.val_ids[index])
+
+    @property
+    def column_names(self):
+        column_names = ['image', 'mask']
+        return column_names
+
+    def __len__(self):
+        if self.is_train:
+            return len(self.train_ids)
+        return len(self.val_ids)
+
+
 def get_args():
     parser = argparse.ArgumentParser(description='Preprocess the UNet dataset ',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -42,5 +96,8 @@ def get_args():
 if __name__ == '__main__':
     args = get_args()
 
-    preprocess_dataset(data_dir=args.data_url, cross_valid_ind=cfg_unet['cross_valid_ind'], cfg=cfg_unet, result_path=
-                       args.result_path)
+    if 'dataset' in cfg_unet and cfg_unet['dataset'] == "Cell_nuclei":
+        cell_dataset = CellNucleiDataset(args.data_url, 1, args.result_path, False, 0.8)
+    else:
+        preprocess_dataset(data_dir=args.data_url, cross_valid_ind=cfg_unet['cross_valid_ind'], cfg=cfg_unet,
+                           result_path=args.result_path)

model_zoo/official/cv/unet/scripts/run_infer_310.sh

@@ -14,9 +14,10 @@
 # limitations under the License.
 # ============================================================================
 
-if [[ $# -lt 2 || $# -gt 3 ]]; then
-    echo "Usage: bash run_infer_310.sh [MINDIR_PATH] [DATA_PATH] [DEVICE_ID]
-    DEVICE_ID is optional, it can be set by environment variable device_id, otherwise the value is zero"
+if [[ $# -lt 3 || $# -gt 4 ]]; then
+    echo "Usage: bash run_infer_310.sh [MINDIR_PATH] [DATA_PATH] [DEVICE_ID] [NEED_PREPROCESS]
+    DEVICE_ID is optional, it can be set by environment variable device_id, otherwise the value is zero.
+    NEED_PREPROCESS means weather need preprocess or not, it's value is 'y' or 'n'."
 exit 1
 fi
 
@@ -29,7 +30,7 @@ get_real_path(){
 }
 model=$(get_real_path $1)
 data_path=$(get_real_path $2)
-if [ $# == 3 ]; then
+if [ $# == 4 ]; then
     device_id=$3
     if [ -z $device_id ]; then
         device_id=0
@@ -37,10 +38,12 @@ if [ $# == 3 ]; then
         device_id=$device_id
     fi
 fi
+need_preprocess=$4
 
 echo "mindir name: "$model
 echo "dataset path: "$data_path
 echo "device id: "$device_id
+echo "need preprocess or not: "$need_preprocess
 
 export ASCEND_HOME=/usr/local/Ascend/
 if [ -d ${ASCEND_HOME}/ascend-toolkit ]; then
@@ -85,7 +88,7 @@ function infer()
     fi
     mkdir result_Files
     mkdir time_Result
-    ../ascend310_infer/src/main --mindir_path=$model --dataset_path=./preprocess_Result/ --device_id=$device_id &> infer.log
+    ../ascend310_infer/src/main --mindir_path=$model --dataset_path=./preprocess_Result/ --device_id=$device_id --need_preprocess=$need_preprocess &> infer.log
 }
 
 function cal_acc()